The Doctor's Choice
by storiesandabsurdities
Summary: When faced with the Library once more, the Doctor must make a heartbreaking choice.
1. The Abduction

The familiar engines of the TARDIS wailed on as the Doctor stood at the console. He had his head bowed, standing calmly and leaning against the console, letting out a sigh. He'd dropped Amy and Rory back off in Leadworth. They were safer there; happier there. Amy hadn't put up much of a fight, but he could see it in her eyes. She felt hurt, betrayed even, but he just couldn't keep putting her life in danger. He couldn't see Rory die anymore than he already had. He knew that there would be one time where he wouldn't wake up, and Amy would never forgive him. He would never forgive himself.

The phone on the console let out a shrill ring. The Doctor jumped back a little, startled by the sudden sound interrupting his thoughts. He looked at the phone for a few more rings before picking it up slowly. There were only a handful of people in the universe that had that number. He placed the phone to his ear.

"Hello?" He asked tentatively.

"D-doctor,"

The voice was one he recognized. It was the voice of one of the people he'd just been thinking about. _Rory. _But his voice sounded distressed. The Doctor pressed the phone more firmly to his ear, as if it brought his concern closer to the person talking on the other end.

"Rory? Rory, what's wrong?"

"Doctor, it's… it's A-amy."

His heart stopped. _Amy. _Mad, impossible Amy. Rory's voice didn't sound good; not good at all. He wasn't calling to tell him that she was pregnant again. He wasn't calling to say her perfume had taken to new heights. No, this was bad. This was very bad.

"What about Amy? Come on. Talk to me, Rory. What's happened to Amy?"

"She—she's gone."

"Gone? What do you mean gone?"

There was a flickering sound, like a screen coming to life. The Doctor looked up at the TARDIS screen but it was blank. The flickering continued for a few more moments before the Doctor lowered the phone from his ear and turned around. There was a silhouette of a woman that was starting to materialize a few feet away from him. He could hear Rory calling for him from the phone but it dropped out of his hand. The woman came into view now and he knew her face; eye patch and all.

"Kovarian."

The Kovarian hologram gave him a wicked smile. "He_llo, _darling Doctor. Miss me?"

"Can't say that I did…"

The Doctor purses his lips together and rubs his hands over his face. He can still faintly hear Rory calling something into the phone but he can't pick it up. Not now. He would get to Rory later. He knew the moment she appeared why she was here.

He let out a long breath, attempting to control the anger building up inside him. "What have you done with Amelia?"

Kovarian lets out a shrill sinister giggle. "Oh, so quick. What have I done with Amelia? Poor little beautiful Amelia Pond. You're never there to save her, are you?"

"I am giving you a chance now. Tell me what you did with Amy or I will trace the signal to your hologram and _make _you tell me." The Doctor's voice is scarily even.

"You'll never find little Amelia with that kind of talk." The hologram pulls out what looks like a small tablet and smirks. "She needs you now more than ever. Wondering how I managed to snatch her from under your nose again? It's not hard. You dropped her and that husband of hers off in Leadworth thinking they'd be safe. How cute." She pauses. "I waited for her little husband to work the night shift and took her in her sleep. She's waking up now though."

The Doctor let out another long breath. "Where is she, Kovarian? I am _not _kidding."

"I'll send the video feed to your screen, darling." She lifts her hand. "I'll be in touch."

The hologram snaps its fingers and it disappears before his eyes. It only takes a few seconds before the screen on the TARDIS flickered to life. It shows a close up of Amy's face. Her hair is sprayed out around her and her eyes are starting to open. The shot pans out and he breathes a sigh of relief. She looks unharmed. He can't make out where she is though. But suddenly there was a voice.

A voice that he would remember as long as he lived. The camera panned away from Amy and over to a what would look like a statue to any other person but the Doctor knew what it was. He knew who it was. As it got closer, he saw the face placed on it. The face of his wife—River, who was doomed to life as a data ghost. Her face is expressionless; her voice unfeeling.

"The Library has been breached. Others are coming."

The Doctor scrambled away from the screen and grabbed the phone from where it had fallen from his hand. He held it up to his ear and he could hear Rory's quiet sobs. He attempted to keep his voice even as he spoke.

"Rory. Get ready. I'm coming to get you. We need to get to Amy… and fast."


	2. The Message

Rory sat on the front steps of his house. He couldn't bear to be inside in without Amy there. He had something small and black that he was twisting in his hands. It had been lying on the bed when he'd gotten home from work early that morning. It was how he knew that Amy had been taken, rather than just out for the day. He let out a long breath as tears started to sting his eyes. He was never there when she needed him. He was always letting her down.

He rubbed his hands over his face and wiped his eyes. He didn't have time to be upset now. Amy needed him. He'd come out to the steps two hours ago to wait for the Doctor and each minute felt like another crack in his head. It was another minute Amy was all alone where ever she was. It might be one minute she couldn't spare. He stood up and kicked at the railing. Where was he?

Just as the thought left his mind, he heard a familiar sound. _Vworp, vworp, vworp. _He turned away from the house to see the TARDIS materializing on a corner down the road. He didn't hesitate. He took off in a sprint down the street to the police box and when the door swung open, he didn't wait for the Doctor to step out. He charged right in, slamming the door behind him and heading to the console. The Doctor followed behind him tentatively.

Rory rubbed his face with his hands. "Okay, now… where exactly is Amy?"

"Now, Rory… I don't want you to…"

Rory let out an exasperated sound, flinging the small, black object at the Doctor in frustration. The Doctor just barely caught it and examined it in the light. It was a black eye patch, identical to the one that Kovarian wore. The Doctor let out a sigh as Rory continued.

"I know she has her. I know what that means." He points to the eye patch. "Now, I'll ask you again… where is my wife?"

The Doctor lets out a sigh as he sets the eye patch down on the console. He pulls the screen over so it sits in front of him and starts punching things out on a keyboard. To Rory, it looked like nothing but a random set of letters and numbers but it must mean something because the screen started to make a beeping noise. He waited patiently for a few moments while the Doctor typed. When he was done, he turned to Rory with expression that was impossible to read.

"Amy's—Amy's in the Library, Rory."

The library? What was so dangerous about a library? "Eh—I'm afraid that I don't follow…"

"This isn't like your human libraries. Well, actually, it is. It's an entire planet full of books. The whole planet is one giant library. Every book that's ever been written or will be written is there. But, it's not a good place anymore. It's completely vacant of life now…"

The Doctor paused, rubbing his hand on his neck nervously. When he didn't continue after several minutes, Rory let out another sigh. "Well. Are you going to tell me why?"

"Because of the Vashta Nerada." The Doctor looked down. "They're… alien. Flesh eating aliens that hide in the shadows. When a human steps into a shadow containing the Vashta Nerada… they become a pile of bones within seconds."

Rory felt his heart sink to his stomach. "So you mean… Amy, she's… with… and she doesn't know…?"

"Yes. I'm afraid so. I know that sounds bad." The Doctor spins on his heels back to the monitor. "Mostly because it is, but I've managed to hack into the main frame of the computer system keeping the Library operational. I have control of the sound system. I can get a message to Amy through there until I can lock the TARDIS onto the Library's coordinates."

Rory gave a solemn nod as he went to stand behind the Doctor. He understood what he was saying but that didn't make him feel any better. Amy was all alone, in that horrible Library and she didn't even know how dangerous it was. How close she was to… He couldn't even think it. He took a deep breath in, steadying himself as the Doctor punched in the last bit of coding and a video feed of Amy popped onto the screen.

He couldn't help but think she looked beautiful. Her hair was gently tousled, like it always was when she awoke from slumber and her face was breathtaking, even though it hurt him to see it so twisted with fear. She kept spinning around, looking like she might be searching for an enemy. Little did she know the enemy was so close… she just couldn't see it.

"Amelia Pond! Amelia, can you hear me?" The Doctor called into a microphone on the console.

Amy's head snapped up, searching for the source of his voice. "…Doctor?"

"Yes, yes. It's me. You can't see me but I can see you."

"Doctor, I'm scared." Her voice cracked a little, still looking around the room.

"You're in danger, of course you're scared. Now shut up and listen to me. Amelia, this is very important. Count the shadows. Always count the shadows and stay in the light. If you walk into the shadows, you're dead. Period. I won't be able to bring you back."

Amy's eyes widen in terror as she steps back further into the light. "What's in the shadows?"

"Something that will kill you, Amy, now don't worry about what they're called." The Doctor answered a bit roughly.

"Oi, cool it, will you!" Rory responded angrily. "She's scared out of her wits."

Amy's expression softens considerably. "Rory? Rory, is that you?"

Rory grabs the microphone out of the Doctor's hand. "Yes, Amy, darling. It's me."

"I love you." She says shakily.

Rory feels tears coming to his eyes. "No, now don't you do that. Don't you dare say your goodbyes to me, Amelia Pond. I'm coming for you. I always come for you. You know that."

"I do."

"I'll save you, Amy. I promise you that. I will."

She nods, a stray tear going down her face. "I trust you."

"I love you, Amy. So much."

The Doctor takes the microphone back from Rory gently. "We're coming for you, Amy. Stay strong for me and stay out of the shadows. Whatever you do, stay out of the shadows."

The TARDIS screen flickers off, leaving Rory with one last image of Amy standing in the only light in the room, looking terrified and alone. He wipes the tears from his face and clears his throat. He would save her. He would. He promised and he would. He always did.

The Doctor set the microphone down and went jumping around the console at a furious speed. He was punching in coordinates and flipping levers with determination. He was muttering quietly to himself. Rory could see he would only be in his way. He sat down in the chair closest to the console and braced himself as the Doctor threw up the last lever and the TARDIS jerked into action.

Not quickly enough it seemed, the TARDIS finally jerked to a halt and the Doctor looked over at Rory again, rubbing his face with his hands. He looked distraught, much more so than he had when they'd been talking about Amy but Rory couldn't pinpoint a reason why. The Doctor walked past him silently and over to the door swinging it open. Rory walked over and stood by his side peering out into the room. A voice sounded that made him stop cold. The Doctor let out a shaky sigh.

"Hello, and welcome to the Library." The welcome node called out in his daughter's voice.


	3. The Story

Madame Kovarian walked very confidently down the only well lit hallway in the whole Library. Her mouth was curved into a sinister smile, having heard the TARDIS engines as it landed in the main room. She wasn't headed toward the Doctor though, she would have plenty of time for him later. No, she walked away from him, toward a room at the end of the hall. She took a key from her pocket and twisted it in the lock, hearing it click and slipping inside.

The redhead in the middle of the room sat in the middle of the large circle of light. She looked up and Kovarian noted the tear tracks on her face with another small smirk. Oh how the Doctor made himself so vulnerable with his little companions. How easy it was for her to get her hands on Amy… she could have snatched the husband too if she'd wanted. But Amy was the key… she was his best friend.

Amy stood as Kovarian came into the light, a look of disgust on her face. It caused a giggle to pass through Kovarian's tightly pressed lips. "Hello, Amy, dear."

"You. You're the one who brought me here?" Her Scottish accent was still shaking.

"Of course it was me. Who else can get their hands on you this easily?" Kovarian lets out a tsking noise with her tongue. "He doesn't look after you very well, does he?"

Amy shook her head, an angry expression taking over her features. "Don't insult him in front of me."

"Or what, may I ask? I'm sure he's warned you about the Vashta Nerada by now? You can't even come into the shadows… why should I be scared of you?"

"Why isn't anything happening to you? The Doctor said…"

"Oh, lay off that precious Doctor bit, Amy. It's really getting old." Kovarian lets out a sigh. "I'm quarantined. Perfectly safe from the Vashta Nerada. Don't you worry your pretty little head about me."

"I'm not worried about you. Just mildly disappointed."

Kovarian gives a sickly sweet smile. "I came to tell you a story, Amelia. And it's very important that you pay very close attention to it, because there will come a time when the Doctor is given a choice. But it's not just his choice… it's yours and Rory's as well."

She watches as a battle rages over the redhead's face. At first, she looks repulsed and ready to send her away. But then… there it was. A flicker of curiosity. That was all she needed. Amy sighed.

"All right. I'll bite. What's the story?"

"The Doctor came here a number of years ago, when he was still in his tenth regeneration and travelling with a woman by the name of Donna Noble. He met a young archeologist here by the name of River Song. Of course, you know River Song, don't you, Amy?" She asks cruelly.

Amy's face froze. "R-river?"

"Oh yes. It was the first time he'd ever met her but she knew everything about him. Now as a time traveler and a member of River's excellent story, you're not going to be daft enough to ask why. She was from his future, as you well know. But there is a portion of River's story that the Doctor's never told you, Amy and it's this. The Doctor met River Song for the first time right here in the Library but that was the last time that she ever saw him. She died here, protecting the Doctor and stabilizing the Library itself. You know when the Doctor dropped you and Rory off? Did he look sad? Distraught? Did he mention the singing towers? He let River come here to her death. He knew what was happening. She told him before she died."

Kovarian watched as her words sank in. The emotions that crossed Amy's face they ranged from rage to brokenness and everywhere in between. She gave a sad looking smile towards her, letting everything soak in before continuing.

"Luckily, I can save his character a little bit. He did manage to save her. She's still alive, in the main frame of the computer that keeps this Library operational. She's doomed to be a data ghost. Her face has been duplicated and placed on a welcome node right here in the Library."

Amy looked up, her face blank. "She's—she's still alive?"

Kovarian gave a wicked smile. "Of course she is, my dear." She turned back toward the door. "Now, if you'll excuse me, I have to go attend to your Doctor and husband. I hope they can find you before you have to join her."

With another sinister laugh, she exited the room.


	4. The Choice

The Doctor let out a sigh. Hearing her voice again, for the second time that day… it hurt. He flashed back to the Singing Towers; to their last night together. He couldn't tell her. It would have screwed up their whole timeline. No. He had to sit and watch her live her last moments without saying a word. It had killed him, almost literally, and that was when he had decided that Amy and Rory were better off back in Leadworth without him.

He looked over at Rory whose face looked pale white and frightened. He didn't want to push him. He knew that he had recognized the voice. Rory let out a long sigh, rubbing his eyes.

"I… was that-?"

"Rory…" The Doctor started. "I could explain it to you but it would take too much time. Amy. Amy needs us, Rory. Just let me tell you… there's nothing we can do about… that. I know that. But Amy… We can save her, Rory."

Rory shook his head, bringing himself out of the fog. "Right, Amy… Right. Where do we start?"

The Doctor studied his face carefully. He still wasn't okay, he could see that. He would have a horrible story to tell when this was all over. No. He wouldn't think about that now. Amy needed him. They needed to find her. He took his sonic screwdriver out of his pocket and scanned around before he heard the clicking of heels on hard floor. His face shot up and he took a step forward, partially in front of Rory. Kovarian entered the room seconds later, a pleasant smile on her face.

"Hello, Doctor. Face to face at last."

"Kovarian."

"You have a real knack for not dying, don't you? You're always ruining my plans. And to think… poor little Amy wouldn't be in so much danger if you had just died like you were supposed to."

The Doctor's teeth clenched. "She won't be in danger much longer."

"Oh, my darling Doctor. I have this place surrounded. My men are everywhere, but nowhere at all. The Vashta Nerada are the least of poor Amy's worries. But I have a little proposition for you. A… game, if you will. The lives of both your little companions rest on it… as well as your wife's." She gives Rory a pointed look before glancing back to the welcome node still hidden in the shadows.

"Doctor… what is she talking about? Your wife? River…"

The Doctor could see the gears in Rory's head turning. He would come to the wrong conclusion. Human minds always did. They always looked for the worst. He couldn't possibly fathom how difficult that decision had been. How much he wished that he hadn't had to make it at all. That he could have just told River without worrying about unraveling their timeline.

"What's your proposition, Kovarian?"

"Ah, Doctor. If you get to keep your life, I'm not going to make it easy on you. No, not at all. You see, I have this computer programmed to release your darling wife back into your open arms. But of course… there's just a little catch." She looks over at Rory. "Why don't you go get your lovely wife? She's behind the last door on the left. Don't worry about the shadows."

Rory didn't even give the Doctor a sideways glance as he took off down the hallway for Amy. The Doctor watched him go, waiting a few moments before addressing Kovarian again.

"What's the catch?"

"The computer needs two lives in order to release your wife's."

The Doctor looked back to the hallway Rory had just disappeared down. "…no."

"No? You don't want to see River Song again? Your wife. A companion who can actually stay with your forever instead of withering away like those two eventually will."

"I can't… I can't do that. I can't sacrifice them for my own selfish gain."

At that moment, Rory reentered the room with his arms wrapped around a shaken looking Amy. She glanced from Kovarian to the Doctor before she cast her eyes down at the floor. The Doctor rubbed his face with his hands, sighing.

"I'll make this choice a bit faster for you." She turned around toward the shadows. "Shoot the girl."

Before he could make a sound, a gunshot rang out into the air. He watched in horror as a bullet ripped through Amy's stomach. She fell to the ground with a loud shriek. Rory, horrorstruck, bent down beside her, placing her head in his lap, attempting to put pressure on her wound, tears streaming down his face.

"And now the boy."

The Doctor was quicker to react this time. "No!"

But it was still too late. Another shot rang out and a bullet passed through Rory's stomach. He fell to his back beside Amy, bleeding profusely, their ragged breathing almost in harmony. The Doctor ran over to them both, feeling overwhelmed.

"This isn't fair!" He screamed at Kovarian. "They're going to die anyway!"

"I said I'd make your life difficult, Doctor, but I made your choice easy. You can either save them to the computer and get your wife back or lose all three of them forever. Your choice but I'd think quickly. They don't have much time left."

Amy's hand reached up weakly. "D-doctor…"

He grabbed her hand, bending down beside her. "I'm right here, Amy."

"I know… about River…" She took a deep breath, but he could tell she was fading fast. "I can't… you have to… save her… please."

"I can save you, Amy. You and Rory both. River passed me her regenerations that day in Berlin. I can save you both right now."

"Don't… don't you dare… you… save… her…"

He looked over at Rory, who had a look of determination on his face as he laced his fingers with Amy's. His eyes then flickered shut. He didn't have much time left. He had to make this decision quickly.

"Save… her… please…." Amy's voice was getting weaker. "Rory and I… we'll… be okay…"

Tears started to pour down the Doctor's face. "You're my best friend, you know that right?"

"I… do…"

He brought her hand to his lips and kissed it gently. "I love you."

Then he stood back up, looking over at Kovarian with a mixture of distraught and disgust. He nodded his head down toward Amy and Rory. "Save them. Go on."

Kovarian smiled brilliantly, pulling what looked like a white bulky cube from her inner jacket pocket. She scanned it over Amy and Rory, a bright light emminating from it as their bodies disappeared. The Doctor looked away. The welcome node in the corner spoke again, but this time it wasn't in River's voice but a beautiful Scottish accent.

"Amelia Pond has left the Library. Amelia Pond has been saved."

Another node, further away in the corner spoke up as well. "Rory Williams has left the Library. Rory Williams has been saved."

The Doctor's whole body tensed as he heard Kovarian snap her fingers and disappeared in front of his eyes. But then he heard it…another set of heels clicking on the hard floor. He didn't dare to look behind him but hope was building up inside him. He took a deep breath in, closing his eyes.

There was a long moment's pause.

"Hello, sweetie."


End file.
